In this paper we analyse spatial variation in Japanese dialectal lexicon by assembling a set of methodologies using theories in variationist linguistics and GIScience, and tools used in historical GIS. Based on historical dialect atlas data, we calculate a linguistic distance matrix across survey localities. The linguistic variation expressed through this distance is contrasted with several measurements, based on spatial distance, utilised to estimate language contact potential across Japan, historically and at present. Further, administrative boundaries are tested for their separation effect. Measuring aggregate association within linguistic variation can contrast previous notions of dialect area formation by detecting continua. Depending on local geographies in spatial subsets, great circle distance, travel distance and travel times explain a similar proportion of the variance in linguistic distance despite the limitations of the latter two. While they explain the majority, two further measurements estimating contact have lower explanatory power: least cost paths modelling contact before the industrial revolution, based on DEM and seafaring, and a linguistic influence index based on settlement hierarchy. Historical domain boundaries and present day prefecture boundaries are found to have a statistically significant effect on dialectal variation. However, the interplay of boundaries and distance is yet to be identified. We claim that a similar methodology can address spatial variation in other digital humanities, given a similar spatial and attribute granularity.